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Skills

Molecular microbiology
High-throughput sequencing
Microbial ecology
Bioinformatics
Programing
Data visualization

Disclaimer

Made with the R package pagedown.

The source code is available at github.com/gaospecial/cv.

Last updated on 2019-11-04.



Main

Chun-Hui Gao (高春辉)

Ph. D, Microbiology, bioinformatician, data scientist and R user.

I am broadly interested in the data mining, particularly integration and visualization, of biological, industrial and social datasets, which comes from high-throughput screening, Next-Generation Sequqncing (NGS), public databases and so on.

Work Experience

Post-doc Lecturer

College of Resources and Environment

Huazhong Agricultural University

2019 - 2016

Post-doctoral Fellow

School of Life Science

University of Science and Technology of China

2015 - 2013

Lecturer

School of Food and Biological Engineering

Hubei University of Technology

2012

Education

PhD., Microbiology

Huazhong Agricultural University

Wuhan, CN

2012 - 2007

  • Thesis: The characterization of a novel ArsR-type regulator in Mycobacterium tuberculosis and the characterization of molecular basis of isoniazid drug resistance in Mycobacteria

B. S., Biotechnology

Huazhong Agricultural University

Wuhan, CN

2008 - 2004

  • bachelor-master continous program

The SCELSE Summer Course

Singapore Centre for Environmental Life Sciences Engineering

Singapore, SG

2016

土壤微生物新理论新技术研讨会暨培训班

中科院南京土壤所

Nanjing, CN

2018/11/17 - 2018/11/15

“不忘初心,牢记使命”教工党员培训班

韶山干部培训学院

Shaoshan, CN

2018


Research Summary

Professional Competence

Microbiology

  • Transcriptional regulator
  • Drug resistance
  • Pathogenisis
  • Persistance

Microbial ecology

  • Social interaction
  • Co-culture
  • Multispecies biofilm

NGS

  • (meta-)Genomics
  • (meta-)RNA-seq
  • Microbiome
  • ChIP-seq

Bioinformatics

  • Linux
  • Perl
  • R

Visualization

  • ggplot2
  • ggVennDiagram
  • Reproducible research

Skills

  • Write R package
  • Statistics
  • Illustration
  • Bibliometric
  • Data mining

Whole genome protein-protein and TF-promoter interactome in M. tuberculosis

College of Life Science and Technology

Huazhong Agricultural University

2007 - 2009

We used a bacterial two-hybrid method to construct the whole genome protein-protein interaction (PPI) network, and a bacterial one-hybrid method to construct the whole genome transcriptional regulator (TF) - promoter interaction network in M. tuberculosis.

Novel transcriptional regulator in mycobacteria

College of Life Science and Technology

Huazhong Agricultural University

2009 - 2012

  • An ArsR-like transcriptional factor recognizes a conserved sequence motif and positively regulates the expression of phoP in mycobacteria
  • A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis
  • Characterization of a Novel ArsR-Like Regulator Encoded by Rv2034 in Mycobacterium tuberculosis

The intra-action between three RelBE modules and inter-action between RelBE3/SirR

College of Life Science and Technology

Huazhong Agricultural University

2009 - 2014

  • Characterization of the Interaction and Cross-Regulation of Three Mycobacterium tuberculosis RelBE Modules.
  • Characterization of the interaction between a SirR family transcriptional factor of Mycobacterium tuberculosis, encoded by Rv2788, and a pair of toxin-antitoxin proteins RelJ/K, encoded by Rv3357 and Rv3358.

The regulation of secondary metabolite (ε-poly lysine) biosynthesis in Streptomyces albus ZPM

School of Life Science

University of Science and Technology of China

2013 - 2014

  • Identification of genetic variations associated with epsilon-poly-lysine biosynthesis in Streptomyces albulus ZPM by genome sequencing.

The distribution of type III-A CRISPR-Cas system in Staphylococcus aureus clinical isolates

School of Life Science

University of Science and Technology of China

2014 - 2015

  • Identification and functional study of type III-A CRISPR-Cas systems in clinical isolates of Staphylococcus aureus.

The regulatory mechanism of drug susceptibility in mycobacteria

State Key Laboratory of Agricultural Microbiology

Huazhong Agricultural University

2012 - 2019

  • InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
  • OxiR specifically responds to isoniazid and regulates isoniazid susceptibility in mycobacteria
  • Cross-talk between the three furA orthologs in Mycobacterium smegmatis and the contribution to isoniazid resistance

Unearthing the mechanism of soil biofilms

College of Resources and Environment

Huazhong Agricultural University

2016 - 2019

  • Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides
  • Co-culture of soil biofilm isolates enables the discovery of novel antibiotics
  • Divergent Influence to a Pathogen Invader by Resident Bacteria with Different Social Interactions
  • Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization
  • Impact of metal oxide nanoparticles on in vitro DNA amplification


Teaching Experience

RNA-seq从入门到精通

华中农业大学暑期生物信息学培训班

武汉

2018/7/18

土壤生物化学课题组导师宣讲会

undergraduate students

Wuhan, CN

2018/6/8

土壤微生物组

undergraduate students

Wuhan, CN

2018/5/24

土壤中的多物种生物膜

graduated students

Wuhan, CN

2016/12/1


Conferences

Oral presentations

细菌的江湖——土壤微生物互作研究

华中农业大学资源与环境学院博士后交流会

武汉

2018

微生物之间的协作有利于细菌的存活和代谢

全国土壤生物生化与土壤健康学术研讨会

上海

2017

土壤生物膜的形成和群落演替

中国土壤学会第十三次全国会员代表大会

西安

2016

Conference abstract

Divergent influence to pathogen invader by environmental isolates with different social interactions

The 2nd Global Soil Biodiversity Conference

Nanjing, CN

2017


Publifications

  • Citation = 539
  • H-index = 12
  • I10-index = 13

Soil Biofilms: Microbial Interactions, Challenges, and Advanced Techniques for Ex-Situ Characterization

Soil Ecology Letters, 2019, 1(3-4):85-93

N/A

2019

  • Cai, Peng; Sun, Xiaojie; Wu, Yichao; Gao, Chun-Hui; Mortimer, Monika; Holden, Patricia A.; Redmile-Gordon, Marc; Huang, Qiaoyun

Cross-Talk between the Three furA Orthologs in Mycobacterium Smegmatis and the Contribution to Isoniazid Resistance

The Journal of Biochemistry, 2019, 166(3):237-243

N/A

  • Gao, Chun-Hui; Wei, Wen-Ping; Tao, Hui-Ling; Cai, Li-Kai; Jia, Wan-Zhong; Hu, Lihua; Yang, Min

Divergent Influence to a Pathogen Invader by Resident Bacteria with Different Social Interactions

Microbial Ecology, 2019, 77(1):76-86

N/A

  • Gao, Chun-Hui; Zhang, Ming; Wu, Yichao; Huang, Qiaoyun; Cai, Peng

Impact of Metal Oxide Nanoparticles on in Vitro DNA Amplification

PeerJ, 2019, 7:e7228

N/A

  • Gao, Chun-Hui; Mortimer, Monika; Zhang, Ming; Holden, Patricia A.; Cai, Peng; Wu, Shan; Xin, Yuexing; Wu, Yichao; Huang, Qiaoyun

Extraction of Extracellular Polymeric Substances (EPS) from Red Soils (Ultisols)

Soil Biology and Biochemistry, 2019, 135:283-285

N/A

  • Wang, Shuang; Redmile-Gordon, Marc; Mortimer, Monika; Cai, Peng; Wu, Yichao; Peacock, Caroline L.; Gao, Chun-Hui; Huang, Qiaoyun

Soil Biofilm Formation Enhances Microbial Community Diversity and Metabolic Activity

Environment International, 2019, 132:105116

N/A

  • Wu, Yichao; Cai, Peng; Jing, Xinxin; Niu, Xueke; Ji, Dandan; Ashry, Noha Mohamed; Gao, Chun-Hui; Huang, Qiaoyun

OxiR Specifically Responds to Isoniazid and Regulates Isoniazid Susceptibility in Mycobacteria

FEMS Microbiology Letters, 2019

N/A

  • Yang, Min; Zhang, Li; Tao, Hui-Ling; Sun, Yuan-Chao; Lou, Zhong-Zi; Jia, Wan-Zhong; Hu, Li-Hua; Gao, Chun-Hui

Impact of Soil Clay Minerals on Growth, Biofilm Formation, and Virulence Gene Expression of Escherichia Coli O157:H7

Environmental Pollution, 2018, 243:953-960

N/A

2018

  • Cai, Peng; Liu, Xing; Ji, Dandan; Yang, Shanshan; Walker, Sharon L.; Wu, Yichao; Gao, Chun-Hui; Huang, Qiaoyun

Co-Culture of Soil Biofilm Isolates Enables the Discovery of Novel Antibiotics

bioRxiv, 2018, 353755

N/A

  • Gao, Chun-Hui; Cai, Peng; Li, Zhunjie; Wu, Yichao; Huang, Qiaoyun

Towards a Better Understanding of the Aggregation Mechanisms of Iron (Hydr)Oxide Nanoparticles Interacting with Extracellular Polymeric Substances: Role of pH and Electrolyte Solution

Science of The Total Environment, 2018, 645:372-379

N/A

  • Lin, Di; Cai, Peng; Peacock, Caroline L.; Wu, Yichao; Gao, Chun-Hui; Peng, Wanxi; Huang, Qiaoyun; Liang, Wei

Metabolism, Survival, and Gene Expression of Pseudomonas Putida to Hematite Nanoparticles Mediated by Surface-Bound Humic Acid

Environmental Science: Nano, 2018

N/A

  • Ouyang, Kai; L. Walker, Sharon; Yu, Xiao-Ying; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng

Recent Advances in Microbial Electrochemical System for Soil Bioremediation

Chemosphere, 2018, 211:156-163

N/A

  • Wu, Yichao; Jing, Xinxin; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng

Survival of Escherichia Coli O157:H7 in Various Soil Particles: Importance of the Attached Bacterial Phenotype

Biology and Fertility of Soils, 2017, 53(2):209-219

N/A

2017

  • Liu, Xing; Gao, Chun-Hui; Ji, Dandan; Walker, Sharon L.; Huang, Qiaoyun; Cai, Peng

Bacillus Subtilis Biofilm Development in the Presence of Soil Clay Minerals and Iron Oxides

npj Biofilms and Microbiomes, 2017, 3(1):4

N/A

  • Ma, Wenting; Peng, Donghai; Walker, Sharon L.; Cao, Bin; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng

Effects of Humic Acid on the Interactions between Zinc Oxide Nanoparticles and Bacterial Biofilms

Environmental Pollution, 2017

N/A

  • Ouyang, Kai; Yu, Xiao-Ying; Zhu, Yunlin; Gao, Chun-Hui; Huang, Qiaoyun; Cai, Peng

Metal-Free Inactivation of E. Coli O157:H7 by Fullerene/C3N4 Hybrid under Visible Light Irradiation

Ecotoxicology and Environmental Safety, 2017, 136:40-45

N/A

  • Ouyang, Kai; Dai, Ke; Chen, Hao; Huang, Qiaoyun; Gao, Chun-Hui; Cai, Peng

自然环境中的多物种生物膜:研究方法及社群相互作用

农业资源与环境学报, 2017, (01):6-14

N/A

  • 孙晓洁; 高春辉; 黄巧云; 蔡鹏

大肠杆菌表面感应机制研究进展

浙江大学学报(农业与生命科学版), 2017, (06):685-690

N/A

  • 王立亮; 高春辉; 吴一超; 黄巧云; 蔡鹏

Identification and Functional Study of Type III-A CRISPR-Cas Systems in Clinical Isolates of Staphylococcus Aureus

International Journal of Medical Microbiology, 2016, 306(8):686-696

N/A

2016

  • Cao, Linyan; Gao, Chun-Hui; Zhu, Jiade; Zhao, Liping; Wu, Qingfa; Li, Min; Sun, Baolin

Identification of Genetic Variations Associated with Epsilon-Poly-Lysine Biosynthesis in Streptomyces Albulus ZPM by Genome Sequencing

Scientific Reports, 2015, 5:9201

N/A

2015

  • Wang, Lin; Gao, Chun-Hui; Tang, Nan; Hu, Songnian; Wu, Qingfa

InbR, a TetR Family Regulator, Binds with Isoniazid and Influences Multidrug Resistance in Mycobacterium Bovis BCG

Scientific Reports, 2015, 5:13969

N/A

  • Yang, Min; Gao, Chun-Hui; Hu, Jialing; Zhao, Lei; Huang, Qiaoyun; He, Zheng-Guo

A Novel marRAB Operon Contributes to the Rifampicin Resistance in Mycobacterium Smegmatis

PLoS ONE, 2014, 9(8):e106016

N/A

  • Zhang, Haiwei; Gao, Long; Zhang, Jiaoling; Li, Weihui; Yang, Min; Zhang, Hua; Gao, Chun-Hui; He, Zheng-Guo

Characterization of a Novel ArsR-Like Regulator Encoded by Rv2034 in Mycobacterium Tuberculosis

PloS One, 2012, 7(4):e36255

N/A

2012

  • Gao, Chun-Hui; Yang, Min; He, Zheng-Guo

A TetR-like Regulator Broadly Affects the Expressions of Diverse Genes in Mycobacterium Smegmatis

Nucleic Acids Research, 2012, 40(3):1009-1020

N/A

  • Yang, Min; Gao, Chun-Hui; Cui, Tao; An, Jingning; He, Zheng-Guo

An ArsR-like Transcriptional Factor Recognizes a Conserved Sequence Motif and Positively Regulates the Expression of phoP in Mycobacteria

Biochemical and Biophysical Research Communications, 2011, 411(4):726-731

N/A

2011

  • Gao, Chun-Hui; Yang, Min; He, Zheng-Guo

Global Protein-Protein Interaction Network in the Human Pathogen Mycobacterium Tuberculosis H37Rv

Journal of Proteome Research, 2010, 9(12):6665-6677

N/A

2010

  • Wang, Yi; Cui, Tao; Zhang, Cong; Yang, Min; Huang, Yuanxia; Li, Weihui; Zhang, Lei; Gao, Chun-Hui; He, Yang; Li, Yuqing; Huang, Feng; Zeng, Jumei; Huang, Cheng; Yang, Qiong; Tian, Yuxi; Zhao, Chunchao; Chen, Huanchun; Zhang, Hua; He, Zheng-Guo

Characterization of the Interaction and Cross-Regulation of Three Mycobacterium Tuberculosis RelBE Modules

PLoS ONE, 2010, 5(5):e10672

N/A

  • Yang, Min; Gao, Chun-Hui; Wang, Yi; Zhang, Hua; He, Zheng-Guo

Dissecting Transcription Regulatory Pathways through a New Bacterial One-Hybrid Reporter System

Genome Research, 2009, 19(7):1301-1308

N/A

2009

  • Guo, Manman; Feng, Hui; Zhang, Jun; Wang, Wenqin; Wang, Yi; Li, Yuqing; Gao, Chun-Hui; Chen, Huanchun; Feng, Ying; He, Zheng-Guo

Archaeal Eukaryote-like Orc1/Cdc6 Initiators Physically Interact with DNA Polymerase B1 and Regulate Its Functions

Proceedings of the National Academy of Sciences, 2009, 106(19):7792-7797

N/A

  • Zhang, Lu; Zhang, Lei; Liu, Yi; Yang, Shifan; Gao, Chun-Hui; Gong, Hongchao; Feng, Ying; He, Zheng-Guo